Hi Kate
can you run:
cd /home/fsuser/host/Sprachlernen/Subjects/Y03/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz
and send us the full screen output?
thanks
Bruce
On Tue, 14 Oct 2014, Kate
Riggall wrote:
Hello,
I am using freesurfer for the first time, and I am having issues when I try to
run recon-all for my first subject. My details are:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Debian version: jessie/sid
Kernel info: Linux 3.13.0-37-generic i686
Subject name: Y03
Command line: fsuser@xubuntu-VirtualBox:~/host/Sprachlernen$ recon-all -all
-subjid Y03
Error message: "recon-all exited with ERRORS at Fri Oct 10 02:42:23 EDT 2014"
recon-all.log: attached.
I am running freesurfer within Virtual Box on a windows host, and my subjects
folder is in a shared folder
/home/fsuser/host
and is called
/home/fsuser/host/Sprachlernen/Subjects
I first mounted this shared folder by entering
sudo mount -t vboxsf Kate /home/fsuser/host
and then designated this as my subjects folder by entering
export SUBJECTS_DIR=/home/fsuser/host/Sprachlernen/Subjects
I then created the subject data directory using
recon-all -i Y03_1 -i Y03_2 -subjid Y03
before running recon-all -all. Any assistance would be much appreciated.
Kind regards,
Kate Riggall
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